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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttgtgatttttgtgcaagtcgtgggctacactgtcctttaaggatgcgacagagttgttgctctctagctgatttgttttgctgcggggtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGAATCTCCGGGACCGTGTCACTGGAATCCGGTTTCAGAGCAATA

Basic information

species Physcomitrella patens
transcript PP1S62_157V6.2
intron # 1
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|18345934|gb|BJ177977.1|BJ177977
EST:     ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCT                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|162156416|gb|FC332648.1|FC332648
EST:     GCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCT                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: GCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|162168654|gb|FC343916.1|FC343916
EST:     GCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCT                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: GCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|18329065|gb|BJ161071.1|BJ161071
EST:     ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCT                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|18358713|gb|BJ190772.1|BJ190772
EST:     ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCT                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|100375682|gb|BY968157.1|BY968157
EST:     ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCT                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|18358530|gb|BJ190589.1|BJ190589
EST:     ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCT                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|18343769|gb|BJ175807.1|BJ175807
EST:     ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCT                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|18371305|gb|BJ202907.1|BJ202907
EST:     ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCT                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|18326677|gb|BJ158676.1|BJ158676
EST:     ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCT                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|18346948|gb|BJ178993.1|BJ178993
EST:     GTTTTTTCGGCGTTGCGCATCCCT                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: GTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|208352746|gb|DC905880.1|DC905880
EST:     ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCT                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|100379666|gb|BY949883.1|BY949883
EST:     ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCT                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
EST: gi|18347535|gb|BJ179582.1|BJ179582
EST:     ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCT                         AATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA
genomic: ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 32 (downstream exon)
Score: 40

ACAGCTGATAGTGTTTGTTTTTTCGGCGTTGCGCATCCCTgtgagctcgt ... gtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGAATCTCCGGGACCGTGTCACTGGAATCCGGTTTCAGAGCAATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcgacagagttgttgctctctagctgatttgttttgctgcggggtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGAATCTCCGGGACCGTGTCACTGGAATCCGGTTTCAGAGCAATA
                       agctgat  putative branch site (score: 40)
                            atttgtttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttgtgatttttgtgcaagtcgtgggctacactgtcctttaaggatgcgacagagttgttgctctctagctgatttgttttgctgcggggtatttgcagAATAATATTGCTCCGAAAGTCATGGCTCTGAAGACAGCAGCCATGACAGGAATCTCCGGGACCGTGTCACTGGAATCCGGTTTCAGAGCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA